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. 2018 Nov 27;9:5004. doi: 10.1038/s41467-018-07446-w

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — Dxz4, Firre, and Xi-specific superloops. a Reciprocal interaction between Dxz4 and Firre in post-XCI fibroblasts. Top: 4C interaction profiles with the core of the Firre tandem repeat as the viewpoint. Bottom: 4C interaction profiles with the core of the Dxz4 tandem repeat as the viewpoint. Black: all unique reads (comp). Grey: repetitive (non-unique) reads (reps). Blue: Xa (cas)-specific reads. red: Xi (mus)-specific reads. Note: For all tracks and Hi-C datasets, “comp” (“complete”) refers to all unique reads, including non-allelic reads. “reps” refers to all non-unique reads. b 4C from a unique, allele-specific viewpoint at the 3′ end of Firre in cells with either an inactive mus (cas Xa/mus Xi) or an inactive cas (cas Xi/mus Xa). Red: interaction profile for unique (comp) reads on the mus allele. Blue: interaction profile for unique (comp) reads on the cas allele. Pink: interaction profile for non-unique (reps) reads from the mus allele. Light Blue: interaction profile for non-unique (reps) reads from the cas allele. Positions of Firre, Dxz4 and Xist are shaded light grey and indicated with red bars. c 4C interaction profile from a unique, allele-specific viewpoint at the 3’ end of Firre in cells with either a mus Xi (top tracks) or a cas Xi (bottom tracks), zoomed in onto Dxz4. Light blue: interaction profile from the cas Firre viewpoint. Pink: interaction profile from the mus Firre viewpoint. d 4C interaction profile over Firre using the Dxz4 core viewpoint in cells either with a mus Xi (top tracks) or a cas Xi (bottom tracks). Black: all unique (comp) reads. Grey: non-unique (repetitive) reads. Blue: cas reads. Red: mus reads. Note: c and d zoom into Dxz4 and Firre respectively to better highlight the allele-specific superloop interactions. The IgV browser’s windowing function can obscure the relative Xa:Xi interaction strength at large length scales (such as in a), thus these zoomed views allow better comparison of the Xa:Xi ratios